[MAINT] Use ruff for linting #113

arokem · 2025-09-19T21:42:23Z

No description provided.

Copilot

Pull Request Overview

This PR introduces ruff as the primary linting tool for the project, replacing the previous linting setup. The changes modernize the development workflow by configuring ruff for both linting and formatting, along with pre-commit hooks for automated code quality checks.

Configures ruff linting rules and target Python version in pyproject.toml
Sets up pre-commit hooks for ruff linting/formatting and codespell checking
Updates build system requirements to use more recent setuptools versions

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
pyproject.toml	Adds ruff configuration with linting rules and updates build system requirements
.pre-commit-config.yaml	Introduces pre-commit hooks for ruff and codespell
.codespellrc	Configures codespell to skip setup.cfg file
setup.cfg	Adds setuptools version requirement

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pyproject.toml

arokem · 2025-09-19T21:43:09Z

I am hoping that this will be part of an overhaul/modernization of our installation machinery so that we can finally get rid of the setup.py file.

36000 · 2025-09-19T21:44:45Z

LGTM

arokem · 2025-09-19T21:44:58Z

This should follow merge of #103, so we don't end up in a sticky situation.

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

arokem · 2025-12-19T19:12:36Z

This PR now implements a range of changes that are the result of running uv run ruff check --fix. I think that most of these changes are in reordering the imports in many different files to comply with ruff rules, but there are potentially many other changes lurking, so a close look even after we let copilot review this again, would be great.

Copilot

Pull request overview

Copilot reviewed 106 out of 107 changed files in this pull request and generated 5 comments.

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pyproject.toml

Copilot · 2025-12-19T19:14:58Z

AFQ/api/group.py

 # -*- coding: utf-8 -*-# -*- coding: utf-8 -*-
-import warnings
 import tempfile
+import warnings

+import AFQ.api.bundle_dict as abd
 from AFQ.definitions.mapping import SynMap
 from AFQ.definitions.utils import Definition
-import AFQ.api.bundle_dict as abd
+
 warnings.simplefilter(action='ignore', category=FutureWarning)  # noqa

+import glob
+import json
 import logging
-from AFQ.api.participant import ParticipantAFQ
-from AFQ.api.utils import (
-    check_attribute, AFQclass_doc,
-    export_all_helper, valid_exports_string)
-import AFQ.utils.streamlines as aus
-from AFQ.viz.utils import get_eye
-from AFQ.data.utils import aws_import_msg_error
-from AFQ.definitions.utils import find_file
-
-from dipy.utils.parallel import paramap
-from dipy.io.stateful_tractogram import StatefulTractogram, Space
-import dipy.tracking.streamlinespeed as dps
-import dipy.tracking.streamline as dts
-from dipy.io.streamline import save_tractogram
-
-from AFQ.version import version as pyafq_version
-from AFQ.viz.utils import trim
-import pandas as pd
-import pydra
-import numpy as np
 import os
 import os.path as op
-from tqdm import tqdm
-import json
 from time import time
+
+import dipy.tracking.streamline as dts
+import dipy.tracking.streamlinespeed as dps
 import nibabel as nib
+import numpy as np
+import pandas as pd
+import pydra
+from bids.layout import BIDSLayout, BIDSLayoutIndexer
+from dipy.io.stateful_tractogram import Space, StatefulTractogram
+from dipy.io.streamline import save_tractogram
+from dipy.utils.parallel import paramap
 from PIL import Image
-import glob
+from tqdm import tqdm
+
+import AFQ.utils.streamlines as aus


The import order is incorrect. Local imports from AFQ modules (lines 5-7) appear before the warnings.simplefilter call, which itself appears before other stdlib imports (lines 11-16). All stdlib imports should be grouped together at the top, followed by third-party imports, and then local imports. The warnings.simplefilter configuration should come after all imports.

AFQ/api/group.py

Copilot · 2025-12-19T19:14:59Z

.pre-commit-config.yaml

+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3


The ruff version in the pre-commit config (v0.4.3) is from April 2024 and is outdated. Since the knowledge cutoff is January 2025, consider updating to a more recent version of ruff-pre-commit to benefit from bug fixes and improvements.

Suggested change

rev: v0.4.3

rev: v0.7.2

Copilot · 2025-12-19T19:14:59Z

AFQ/recognition/tests/test_rois.py

-    check_sls_with_inclusion,
-    check_sl_with_exclusion)
+
+import AFQ.recognition.roi as abr


Module 'AFQ.recognition.roi' is imported with both 'import' and 'import from'.

We are currently getting a few of these: ``` ../../../opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/AFQ/tests/test_api.py:235 /opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/AFQ/tests/test_api.py:235: PytestUnknownMarkWarning: Unknown pytest.mark.nightly_custom - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html @pytest.mark.nightly_custom ```

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 107 out of 108 changed files in this pull request and generated 9 comments.

Comments suppressed due to low confidence (1)

AFQ/definitions/image.py:679

This class does not call ScalarImage.init during initialization. (ThresholdedScalarImage.init may be missing a call to a base class init)

class ThresholdedScalarImage(ThresholdMixin, ScalarImage):

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Copilot · 2025-12-20T00:37:51Z

examples/howto_examples/cloudknot_hcp_example.py

    # set logging level to your choice
    logging.basicConfig(level=logging.INFO)
-    log = logging.getLogger(__name__)
+    log = logging.getLogger(__name__)  # noqa F841


Variable log is not used.

Copilot · 2025-12-20T00:37:52Z

AFQ/nn/synthseg.py

        PVE data with CSF, GM, and WM segmentations.
    """
-    synthseg_labels = {
+    synthseg_labels = {  # noqa: F841


Variable synthseg_labels is not used.

Copilot · 2025-12-20T00:37:52Z

examples/howto_examples/add_custom_bundle.py

+# second gives the layout of the figure (eg. 3 rows 4 columns) and finally is
+# the view.
+
+montage = my_afq.group_montage("L_SLF1", (3, 4), "Sagittal", "left", slice_pos=0.5)


This assignment to 'montage' is unnecessary as it is redefined before this value is used.

Copilot · 2025-12-20T00:37:52Z

examples/howto_examples/add_custom_bundle.py

+# the view.
+
+montage = my_afq.group_montage("L_SLF1", (3, 4), "Sagittal", "left", slice_pos=0.5)
+montage = my_afq.group_montage("L_SLF2", (3, 4), "Sagittal", "left", slice_pos=0.5)


This assignment to 'montage' is unnecessary as it is redefined before this value is used.

Copilot · 2025-12-20T00:37:52Z

AFQ/definitions/image.py

+        as_percentage=False,
+        combine="and",
+    ):
        CombineImageMixin.__init__(self, combine)


This initialization method calls CombineImageMixin.init multiple times, via this call and this call, resolving to CombineImageMixin.init and ThresholdMixin.init respectively.

Suggested change

CombineImageMixin.__init__(self, combine)

Copilot · 2025-12-20T00:37:53Z

AFQ/utils/bin.py

    if logger is not None:
        logger.info("Generating default configuration file.")
-    toml_file = open(toml_file, 'w')
+    toml_file = open(toml_file, "w")


File may not be closed if this operation raises an exception.

Copilot · 2025-12-20T00:37:53Z

AFQ/utils/bin.py

    arg_dict = func_dict_to_arg_dict(func_dict, logger=logger)

-    json_file = open(json_file_our_trk, 'w')
+    json_file = open(json_file_our_trk, "w")


File may not be closed if this operation raises an exception.
File may not be closed if this operation raises an exception.
File may not be closed if this operation raises an exception.

Copilot · 2025-12-20T00:37:53Z

AFQ/utils/bin.py

    json_file.close()

-    json_file = open(json_file_their_trk, 'w')
+    json_file = open(json_file_their_trk, "w")


File may not be closed if this operation raises an exception.
File may not be closed if this operation raises an exception.
File may not be closed if this operation raises an exception.

Copilot · 2025-12-20T00:37:53Z

examples/howto_examples/cloudknot_hcp_example.py

+# there.
 CP = configparser.ConfigParser()
-CP.read_file(open(op.join(op.expanduser('~'), '.aws', 'credentials')))
+CP.read_file(open(op.join(op.expanduser("~"), ".aws", "credentials")))


File is opened but is not closed.

arokem · 2025-12-21T16:54:52Z

I think that maybe I will redo this one, but ignore this rule: https://docs.astral.sh/ruff/rules/unnecessary-collection-call/, because it's really not a performance hit in the overall scheme of things and introduced a lot of changes all over the place that we might not really need.

arokem · 2025-12-21T17:01:47Z

Close in favor of #134

Copilot AI review requested due to automatic review settings September 19, 2025 21:42

Copilot AI reviewed Sep 19, 2025

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pyproject.toml Show resolved Hide resolved

arokem and others added 2 commits December 19, 2025 11:05

Adds pre-commit configuration and codespellrc.

ce39af3

Update pyproject.toml

7544c57

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

arokem force-pushed the ruff branch from 9f2156b to 7544c57 Compare December 19, 2025 19:06

Ruff fixes.

79c7f03

arokem requested a review from Copilot December 19, 2025 19:10

Copilot started reviewing on behalf of arokem December 19, 2025 19:10 View session

Copilot AI reviewed Dec 19, 2025

View reviewed changes

arokem and others added 17 commits December 19, 2025 11:16

Use consistent setuptools requirement.

a842ec7

Update AFQ/api/group.py

bd3bc21

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update ruff version.

f1515be

Merge branch 'ruff' of github.com:arokem/pyAFQ into ruff

15d3df6

Run ruff in the CI.

2e8a339

Allow using f-strings as docstrings

1899404

Ruff fixes and some typos.

554d68d

Fixes formatting and typos.

3654fa2

Ruff formatting and skip some linting.

af58c1b

Ruff formatting.

ec7c37a

Ruff linting in definitions/mapping.py

5a3a4a2

Ruff linting in anistropic index calculation docstring.

a86c6e6

Fix error handling mangled during linting

2c393ee

Lint asym_filtering and add an item to codespellrc to ignore "Reson"

9d0998c

Lint multiaxial.

cbad2bb

Skip linting for unused variable.

403dcd6

arokem added 22 commits December 19, 2025 15:04

Linting in API tests.

06a9725

One more error handling.

7d308ad

Linting in test_definitions.

d392afd

Linting in gputractography.

7877518

Linting in utils/bin.py.

e3e89d9

Eliminate trailing whitespace.

44b02d0

Linting in utils/docs.

afa4a65

Linting in docstring_parser.

8bd58dc

Linting in AFQ/utils/path

c71d111

Linting in AFQ/utils/streamlines.

0b64f5d

Linting in viz/altair

a8768df

Linting in fury_backend.

bcc7f95

Linting in viz/plot.

a5015d1

Linting in plotly_backend.

48179d0

Linting in viz utils

57aa5f5

Ignore docs configuration file in linting.

5fa7dc2

Linting in one of the examples.

bc9765a

Formatting and linting in example.

793902f

Linting formatting in hcp cloudknot example.

5885c51

Fixes in visualization howto.

6c0ac9a

Linting formatting.

654380a

Don't lint the examples.

db1f075

arokem requested a review from Copilot December 20, 2025 00:35

Copilot started reviewing on behalf of arokem December 20, 2025 00:36 View session

Copilot AI reviewed Dec 20, 2025

View reviewed changes

Don't lint the setup file.

0937aa6

arokem mentioned this pull request Dec 21, 2025

MAINT: Add ruff for linting #134

Merged

arokem closed this Dec 21, 2025

[MAINT] Use ruff for linting #113

[MAINT] Use ruff for linting #113

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